DTI Prep Extension

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DTI Prep Extension

Emily Louise Belleau

Hello Slicer Experts,


I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?


I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.


Thanks,


Emily


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Re: DTI Prep Extension

inorton
Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).

If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.

I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.

- bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.

- DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:

'/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'

However, I'm not sure how to specify this path to DTIPrep.


On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Experts,


I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?


I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.


Thanks,


Emily


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: DTI Prep Extension

Francois Budin
Hello Emily,

I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
I think you can select some parameters in the DTI configuration file to not actually use these tools.
Hope this helps,

Francois

On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).

If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.

I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.

- bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.

- DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:

'/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'

However, I'm not sure how to specify this path to DTIPrep.


On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Experts,


I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?


I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.


Thanks,


Emily


_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: DTI Prep Extension

Emily Louise Belleau
In reply to this post by inorton

Thank you so much, this is very helpful!!!


Emily


From: Francois Budin <[hidden email]>
Sent: Thursday, October 6, 2016 4:12:55 PM
To: Isaiah Norton; Martin Styner; [hidden email]
Cc: Emily Louise Belleau; SPL Slicer Users
Subject: Re: [slicer-users] DTI Prep Extension
 
Hello Emily,

I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
I think you can select some parameters in the DTI configuration file to not actually use these tools.
Hope this helps,

Francois

On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).

If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.

I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.

- bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.

- DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:

'/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'

However, I'm not sure how to specify this path to DTIPrep.


On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer Experts,


I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?


I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.


Thanks,


Emily


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: DTI Prep Extension

Martin Styner
In reply to this post by inorton
Dear all

Yes, NITRC forums are the best avenue for such discussions.

Emily, on NITRC you can find also manuals as well as powerpoint-based tutorials:
https://www.nitrc.org/docman/index.php?group_id=283&selected_doc_group_id=2742&language_id=1#folder

Like Francois mentioned, all the external tool usage (or non-usage) can be configured in the DTIPrep protocol.

Martin


--
Martin Styner, PhD. MS ETH
Associate Professor
Neuro Image Analysis and Research Lab
Carolina Institute for Developmental Disabilities
Departments of Psychiatry  and Computer Science
CB 7160, University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7160
Cell:  919 260 6674
Fax:  919 962 1799




> On Oct 6, 2016, at 17:12, Francois Budin <[hidden email]> wrote:
>
> Hello Emily,
>
> I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
> I think you can select some parameters in the DTI configuration file to not actually use these tools.
> Hope this helps,
>
> Francois
>
> [1] https://www.nitrc.org/projects/dtiprep/
>
> On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
> Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).
>
> If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
> - bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.
>
> - DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:
>
> '/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'
>
> However, I'm not sure how to specify this path to DTIPrep.
>
> [1] https://www.nitrc.org/forum/forum.php?forum_id=1188
> [2] http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
> [3] https://www.nitrc.org/projects/mricron 
>
> On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:
> Hello Slicer Experts,
>
>
> I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
>
> Thanks,
>
>
> Emily
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>

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Re: DTI Prep Extension

Emily Louise Belleau
In reply to this post by inorton

Hello DTI Prep Experts,


I noticed that DTI Prep changes some information in the header file.


For example, in the header by sizes it is 75 96 96 64. When before it was  96 96 64 75. Also, under kinds, now it is vector domain domain domain. Before DTI Prep it was space space space list.


I *do* know how to go about changing the header information but was wondering if I should be concerned about this.


Everything else is the same.


Thanks,


Emily


From: Styner, Martin Andreas <[hidden email]>
Sent: Friday, October 7, 2016 9:37:09 AM
To: Francois Budin
Cc: Isaiah Norton; Juan Carlos Prieto; Emily Louise Belleau; Slicer Userlist
Subject: Re: [slicer-users] DTI Prep Extension
 
Dear all

Yes, NITRC forums are the best avenue for such discussions.

Emily, on NITRC you can find also manuals as well as powerpoint-based tutorials:
https://www.nitrc.org/docman/index.php?group_id=283&selected_doc_group_id=2742&language_id=1#folder

Like Francois mentioned, all the external tool usage (or non-usage) can be configured in the DTIPrep protocol.

Martin


--
Martin Styner, PhD. MS ETH
Associate Professor
Neuro Image Analysis and Research Lab
Carolina Institute for Developmental Disabilities
Departments of Psychiatry  and Computer Science
CB 7160, University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7160
Cell:  919 260 6674
Fax:  919 962 1799




> On Oct 6, 2016, at 17:12, Francois Budin <[hidden email]> wrote:
>
> Hello Emily,
>
> I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
> I think you can select some parameters in the DTI configuration file to not actually use these tools.
> Hope this helps,
>
> Francois
>
> [1] https://www.nitrc.org/projects/dtiprep/
>
> On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
> Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).
>
> If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
> - bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.
>
> - DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:
>
> '/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'
>
> However, I'm not sure how to specify this path to DTIPrep.
>
> [1] https://www.nitrc.org/forum/forum.php?forum_id=1188
> [2] http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
> [3] https://www.nitrc.org/projects/mricron
>
> On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:
> Hello Slicer Experts,
>
>
> I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
>
> Thanks,
>
>
> Emily
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>


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Re: DTI Prep Extension

Emily Louise Belleau

Hello DTI Prep Experts,

I noticed that DTI Prep changes some information in the header file.

For example, in the header by sizes it is 75 96 96 64. When before it was  96 96 64 75. Also, under kinds, now it is vector domain domain domain. Before DTI Prep it was space space space list.

I *do* know how to go about changing the header information but was wondering if I should be concerned about this.

Everything else is the same.

I would appreciate any guidance!

Thanks,

Emily


From: slicer-users <[hidden email]> on behalf of Emily Louise Belleau <[hidden email]>
Sent: Monday, February 13, 2017 4:46:47 PM
To: Styner, Martin Andreas; Francois Budin
Cc: SPL Slicer Users; Juan Carlos Prieto
Subject: Re: [slicer-users] DTI Prep Extension
 
This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing Feedback

Hello DTI Prep Experts,


I noticed that DTI Prep changes some information in the header file.


For example, in the header by sizes it is 75 96 96 64. When before it was  96 96 64 75. Also, under kinds, now it is vector domain domain domain. Before DTI Prep it was space space space list.


I *do* know how to go about changing the header information but was wondering if I should be concerned about this.


Everything else is the same.


Thanks,


Emily


From: Styner, Martin Andreas <[hidden email]>
Sent: Friday, October 7, 2016 9:37:09 AM
To: Francois Budin
Cc: Isaiah Norton; Juan Carlos Prieto; Emily Louise Belleau; Slicer Userlist
Subject: Re: [slicer-users] DTI Prep Extension
 
Dear all

Yes, NITRC forums are the best avenue for such discussions.

Emily, on NITRC you can find also manuals as well as powerpoint-based tutorials:
https://www.nitrc.org/docman/index.php?group_id=283&selected_doc_group_id=2742&language_id=1#folder

Like Francois mentioned, all the external tool usage (or non-usage) can be configured in the DTIPrep protocol.

Martin


--
Martin Styner, PhD. MS ETH
Associate Professor
Neuro Image Analysis and Research Lab
Carolina Institute for Developmental Disabilities
Departments of Psychiatry  and Computer Science
CB 7160, University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7160
Cell:  919 260 6674
Fax:  919 962 1799




> On Oct 6, 2016, at 17:12, Francois Budin <[hidden email]> wrote:
>
> Hello Emily,
>
> I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
> I think you can select some parameters in the DTI configuration file to not actually use these tools.
> Hope this helps,
>
> Francois
>
> [1] https://www.nitrc.org/projects/dtiprep/
>
> On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
> Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).
>
> If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
> - bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.
>
> - DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:
>
> '/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'
>
> However, I'm not sure how to specify this path to DTIPrep.
>
> [1] https://www.nitrc.org/forum/forum.php?forum_id=1188
> [2] http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
> [3] https://www.nitrc.org/projects/mricron
>
> On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:
> Hello Slicer Experts,
>
>
> I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
>
> Thanks,
>
>
> Emily
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>


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Batch Scripting

Emily Louise Belleau
In reply to this post by inorton

Hello Slicer experts


I am currently trying to create a batch script for DTI Prep.


I tried making a simple tcsh script (see attached).


Applications/Slicer.app/Contents/Extensions-23774/DTIPrep/lib/Slicer-4.4/cli-modules/../hidden-climodules/DTIPrep: Command not found.


However, this script does work when I do a single subject on the command line.


Perhaps I can't use this type of scripting for Slicer?


I would appreciate any guidance you are willing to offer!


I should say I am running this on a Mac.


Thank you,


Emily

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DTI_Prep_2-3.sh (1K) Download Attachment
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Re: Batch Scripting

inorton
You are missing the leading slash (`/`) on the command path.
Should be:
/Applications/...
^

On Fri, Feb 17, 2017 at 10:18 AM, Emily Louise Belleau <[hidden email]> wrote:

Hello Slicer experts


I am currently trying to create a batch script for DTI Prep.


I tried making a simple tcsh script (see attached).


Applications/Slicer.app/Contents/Extensions-23774/DTIPrep/lib/Slicer-4.4/cli-modules/../hidden-climodules/DTIPrep: Command not found.


However, this script does work when I do a single subject on the command line.


Perhaps I can't use this type of scripting for Slicer?


I would appreciate any guidance you are willing to offer!


I should say I am running this on a Mac.


Thank you,


Emily

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Re: DTI Prep Extension

Andras Lasso-2
In reply to this post by Emily Louise Belleau

ITK’s itk::ImageFileWriter always writes 4D images to NRRD files as (vector domain domain domain). This order and kind of axes are currently hardcoded in itkNrrdImageIO.cxx.

 

If you only use ITK readers and writers then this change should not cause any problems.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Emily Louise Belleau
Sent: February 13, 2017 18:01
To: Styner, Martin Andreas <[hidden email]>; Francois Budin <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Juan Carlos Prieto <[hidden email]>
Subject: Re: [slicer-users] DTI Prep Extension

 

Hello DTI Prep Experts,

 

I noticed that DTI Prep changes some information in the header file.

 

For example, in the header by sizes it is 75 96 96 64. When before it was  96 96 64 75. Also, under kinds, now it is vector domain domain domain. Before DTI Prep it was space space space list.

 

I *do* know how to go about changing the header information but was wondering if I should be concerned about this.

 

Everything else is the same.

I would appreciate any guidance!

 

Thanks,

 

Emily

 


From: slicer-users <[hidden email]> on behalf of Emily Louise Belleau <[hidden email]>
Sent: Monday, February 13, 2017 4:46:47 PM
To: Styner, Martin Andreas; Francois Budin
Cc: SPL Slicer Users; Juan Carlos Prieto
Subject: Re: [slicer-users] DTI Prep Extension

 

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Hello DTI Prep Experts,

 

I noticed that DTI Prep changes some information in the header file.

 

For example, in the header by sizes it is 75 96 96 64. When before it was  96 96 64 75. Also, under kinds, now it is vector domain domain domain. Before DTI Prep it was space space space list.

 

I *do* know how to go about changing the header information but was wondering if I should be concerned about this.

 

Everything else is the same.

 

Thanks,

 

Emily


From: Styner, Martin Andreas <[hidden email]>
Sent: Friday, October 7, 2016 9:37:09 AM
To: Francois Budin
Cc: Isaiah Norton; Juan Carlos Prieto; Emily Louise Belleau; Slicer Userlist
Subject: Re: [slicer-users] DTI Prep Extension

 

Dear all

Yes, NITRC forums are the best avenue for such discussions.

Emily, on NITRC you can find also manuals as well as powerpoint-based tutorials:
https://www.nitrc.org/docman/index.php?group_id=283&selected_doc_group_id=2742&language_id=1#folder

Like Francois mentioned, all the external tool usage (or non-usage) can be configured in the DTIPrep protocol.

Martin


--
Martin Styner, PhD. MS ETH
Associate Professor
Neuro Image Analysis and Research Lab
Carolina Institute for Developmental Disabilities
Departments of Psychiatry  and Computer Science
CB 7160, University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7160
Cell:  919 260 6674
Fax:  919 962 1799




> On Oct 6, 2016, at 17:12, Francois Budin <[hidden email]> wrote:
>
> Hello Emily,
>
> I am adding Martin and Juan Carlos to the conversation as they should be able to give you more information about DTIPrep and how to use it. As Isaiah mentioned, you may want to ask your questions on the NITRC forum and see if there is any documentation about how to use DTIPrep on NITRC [1]. DTIPrep is distributed with a few other executables that it requires. However, as Isaiah said, it does not package bet2 which is part of FSL and DiffusionWeightedVolumeMasking, which is part of Slicer. These tools can be installed independently on your system. You can then set their path in DTIPrep.
> I think you can select some parameters in the DTI configuration file to not actually use these tools.
> Hope this helps,
>
> Francois
>
> [1] https://www.nitrc.org/projects/dtiprep/
>
> On Mon, Oct 3, 2016 at 5:37 PM, Isaiah Norton <[hidden email]> wrote:
> Unfortunately the DTIPrep extension isn't currently available in recent Slicer versions (I think due to some build system changes).
>
> If you don't get any other responses on here, try the DTIPrep forum on NITRC [1] as the main developers may check there more often than the Slicer list.
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
> - bet2 is part of FSL [2], so you may need to install FSL first. Alternatively, for a much smaller download, you could try installing "mricron" [3], which includes bet. Note that the application name in the mricron bundle is "bet", so it might be necessary to rename/link as "bet2" for DTIPrep to use it.
>
> - DiffusionWeightedVolumeMasking is available in the Slicer 4.5.0-1 release bundle. For example if Slicer is installed in your system Applications folder the path would be:
>
> '/Applications/Slicer\ 4.5.app/Contents/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking'
>
> However, I'm not sure how to specify this path to DTIPrep.
>
> [1] https://www.nitrc.org/forum/forum.php?forum_id=1188
> [2] http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET
> [3] https://www.nitrc.org/projects/mricron
>
> On Mon, Oct 3, 2016 at 2:37 PM, Emily Louise Belleau <[hidden email]> wrote:
> Hello Slicer Experts,
>
>
> I am interested in trying out DTIPrep, which I know was/still currently is an extension of slicer (as well as a standalone program). I am running the latest stable slicer version 4.5.0-1 for Mac OS X. I am unable to find DTI Prep through the extensions wizard. Does DTIPrep only work with earlier versions of Slicer?
>
> I have also downloaded DTIPrep as a stand-alone. However, I got an error message saying it was unable to find that programs bet2 and DiffusionWeighted VolumeMasking. I would appreciate any guidance.
>
>
> Thanks,
>
>
> Emily
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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>
>
> _______________________________________________
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> [hidden email]
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>


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